knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
knitr::opts_chunk$set(echo = F, warning = F, message = F)

seu_merge_epi_p007n_strict_epi_p007t_strict_epi_p008n_strict_epi_p008t_strict_epi_p009n1_strict_epi_p009n2_strict_epi_p009t1_strict_epi_p009t2_strict_epi_p012n_strict_epi_p012t_strict_epi_p013n_strict_epi_p013t.rds

Signature scoring

##  [1] "p007n"  "p007t"  "p008n"  "p008t"  "p009n1" "p009n2" "p009t1" "p009t2"
##  [9] "p012n"  "p012t"  "p013n"  "p013t"  "p014n"  "p014t"  "p016n"  "p016t" 
## [17] "p017n"  "p017t" 
## [1] "broad done"
## [1] "morkel done"
## [1] "SMAD done"
## [1] "TNFa done"
## [1] "Wnt done"
## [1] "YAP done"
## [1] "regev done"

Louvain clusters

Cluster marker genes

rank 0 1 10 11 12 13 14 15 16 17 18 2 3 4 5 6 7 8 9
1 SPINK4 CA1 PLA2G2A CA1 RPL12 HSPD1 MT-CO2 CLCA4 RNF43 MT-ND1 LRMP HEXIM1 RPS6 AQP8 CLCA1 MMP7 ZG16 SLC26A3 BEST4
2 ITLN1 FABP1 OLFM4 SELENBP1 RPL37 HMGB1 MT-CO3 AQP8 MT-ND2 MT-CO3 SH2D6 SOX4 RPS3A CLCA4 FCGBP S100A11 MUC2 AQP8 CA7
3 CLCA1 PHGR1 PIGR SLC26A2 TGFBI LDHB XIST SLC26A3 PTPRC MT-ATP8 FYB1 HES1 RPLP1 SLC26A3 SPINK4 LYZ TFF1 CEACAM7 OTOP2
4 TFF3 SELENBP1 LEFTY1 CA2 RPS2 RPL23 MT-ND2 GUCA2B MKI67 MT-CO2 HPGDS HIST1H4C RPL5 SELENOP ITLN1 PERP GSN CLCA4 MT1G
5 WFDC2 MT1M LCN2 MT-CO2 RPS19 RPL21 MT-ND1 GUCA2A MT-ND3 MT-ND3 TRPM5 MAFB RPSA GUCA2A REP15 RPS7 FCGBP SELENOP GUCA2A
6 FCGBP MT2A B3GNT7 FABP1 RPL7A PCCA CXCR4 TMIGD1 MT-ATP8 SYNE2 PLCG2 HIST1H2BG RPL3 CEACAM7 TFF3 RPL7 TFF3 PLAC8 MT1H
7 KLK1 KRT19 GOLM1 MT-CO3 RPL13 SET SRGN CD177 CXCR4 PLCE1 PSTPIP2 Z93241.1 RPL34 ISG15 MUC2 CEACAM6 CD177 ISG15 MT2A
8 MUC2 CA2 SLPI SULT1B1 RPS18 HSP90AB1 ABCG2 SRGN IGLC3 AZGP1 JUN RPS8 ANPEP ST6GALNAC1 PMEPA1 TSPAN1 CEACAM1 SPIB
9 AGR2 CKB SPINK5 MT-ATP8 RPL32 TUBA1B CEACAM7 SCD IGLC2 BMX IER5L RPL10A PLAC8 KLK1 RPL21 ANKRD36C MS4A12 CA4
10 REG4 MT1G ADH1C MT-ND5 RPS16 NCL MT-CO2 CENPF IGKC COL27A1 AL137077.2 RPLP0 CD177 ANO7 RPL23 SYTL2 IFI27 HES4
11 ST6GALNAC1 ADIRF SLC28A2 HSD11B2 RPL35A TOP2A MS4A12 MT-ND4L JCHAIN ALOX5 CSKMT RPS27A IFI27 RAP1GAP ZFAS1 REP15 GUCA2A PCSK1N
12 REP15 MT1E DMBT1 CD24 RPS23 LCN15 SELENOP VIM IGHA1 IFI6 ZFP36L2 RPS24 HIST1H1C SERPINA1 HSP90AB1 CDC42EP3 SLC9A3 FRMD1
13 SPINK1 FXYD3 NXPE4 CHP2 DPEP1 NAP1L1 SGK1 RGS1 HCK HIST1H2AH RPL9 SLC9A3 SPDEF RPL7A SPATS2L TSPAN1 NEURL1
14 SERPINA1 MT1H NUPR1 GPT FOXQ1 PSMA7 MT-CO1 MT-CO3 AVIL LINC01970 RPL6 TSPAN1 RETNLB TM4SF1 SMIM14 KRT20 DMBT1
15 ZG16 MS4A12 SULT1B1 CKB RPL21 RPSA MT-ND3 TSC22D3 ITPR2 SOCS1 RPS4X MS4A12 MT-ND1 RPS21 ENTPD8 ANPEP ADRA2A
16 XBP1 LGALS3 NXPE1 CES2 RPS7 H2AFZ TRPM6 S100A4 IL17RB AL355075.4 RPL32 CA4 ATOH1 RPS4X SCNN1A PHGR1 ADCY5
17 RNASE1 SLC26A3 CFTR PLCE1 RPL6 RPL7A LINC02023 CXCL8 ALOX5AP IER2 RPS14 HPGD HEPACAM2 PPA1 MGLL HPGD MYOM1
18 RPL36 KRT20 AGR2 UGT2B17 RPS20 ENO1 PLAC8 DDIT4 PTPN18 HIST1H2AG TXN GUCA2B SLC4A7 EIF3E MLPH EMP1 CTSE
19 FOSB CEACAM7 GPX2 KRT19 HSP90AB1 GAPDH ANPEP HLA-DRA PTGS1 NRARP RARRES2 MUC12 L1TD1 FTL RAB27A FABP1 NOTCH2
20 HEPACAM2 SLC26A2 PPP1R12B PAPSS2 RPL10A CENPF ABCB1 TNFAIP3 PBXIP1 IER5 RPL13A TMIGD1 MLPH RPL35A RASEF SDCBP2 CDK18
21 RPS24 TMEM54 SI PIGR RPL24 MKI67 MT-ND2 LYZ MATK PPP1R15A RPS12 CDHR5 MT-ND2 ANXA2 KLK1 MISP SLC2A5
22 SPDEF KRT8 AGR3 PHGR1 RPL36 RPS2 SECTM1 CD74 CCSER1 EGR1 RPS7 SDCBP2 ERN2 RPS27A BCAS1 CEACAM6 MEIS1
23 SLC12A2 ETHE1 DUOX2 HMGCS2 S100A11 RPL27 HPGD SH2D7 HIST1H3A RPS19 PRSS3 MUC4 TIMP1 FER1L6 MUC12 OTOP3
24 RPL18A CDKN2B-AS1 PRAC1 SLC4A4 RPS15A RPL6 SLC17A4 GRASP POU3F1 EEF1B2 EMP1 MT-ND3 S100A4 QSOX1 TMPRSS2 C2orf54
25 SH3BGRL3 LGALS4 MUC4 MT-CO1 RPS4X DEK CA4 ANXA13 BTG1 RPS2 SGK1 SYTL2 RPL10 TBX10 SFN UNC5C
26 RPL10 C10orf99 CD24 MAOA RPS12 HMGA1 TMEM37 GNG13 RASD1 RPL18A MISP MT-CO3 RPS20 SERPINA1 TRIM31 PRKG2
27 RPS12 CES2 RNF186 ADIRF RPS21 RAN RARRES3 HTR3E AC023157.3 RPS18 TRIM31 XBP1 RPL12 TPSG1 TMEM54 NBPF14
28 RPLP1 CDHR5 KLF5 LGALS2 RPS27A NPM1 SLC51B HIP1R AL031777.3 RPL23A PKIB FRYL RPL5 SPDEF CA4 DOCK4
29 SSR4 SLC51B TSPAN8 C10orf99 RPL30 RPL19 CDHR5 B4GALNT4 JUNB LEFTY1 CEACAM1 RASD1 PSMA7 GPR153 CA2 NBPF19
30 NR4A1 C2orf88 TNFRSF11A BSG NAP1L1 RPL7 ISG15 OGDHL CITED2 RPL14 RHOC RPS15A MINPP1 MUC13 GUCA2B
31 KLF4 GUCA2A MLEC B3GALT5 RPS8 HSPE1 MUC12 AFAP1L2 HSPA1B RPS5 RARRES3 RPS12 FOXA3 PRSS3 CARD16
32 RETNLB AKR1B10 FAM3D RPL28 PRKDC TSPAN1 RGS13 BTG2 RPL10 CDA COMMD6 DHRS9 PKIB SCIN
33 RPS27 C1QTNF12 S100A11 RPL3 RPS20 EMP1 GRK5 IER3 RPS23 SMPDL3A S100P B3GNT6 CDHR5 HRCT1
34 KIAA1324 PRSS3 RARRES1 PHLDA1 PTMS HIST1H1C SPIB CEBPB RPS15A TMEM37 SCD BEST2 RHOC MSLN
35 FAM3D PKIB MECOM RPL31 SNRPF MIR194-2HG ADGRG6 AL118516.1 ATP5MC1 SLC51B IFITM3 RFLNA PLS1 MT1M
36 IGFBP2 PIGR MUC5B RPL7 TUBB CDA DKK3 HIST1H2BF NACA MEP1A POMP ATOH1 PI3 CDHR2
37 RASD1 BSG MGST2 TESC GSTP1 TRIM31 TUBA1A GADD45B RPS16 SECTM1 BTF3 SMIM5 DHRS9 MT1E
38 RPL14 DHRS11 AKR1C3 ASCL2 RANBP1 MT-ND4L POU2F3 FOSB RPL24 CDHR2 RPL30 CAPN9 MYL12B SAMD9L
39 CDC42EP5 PLAC8 SPINK1 TIMP1 IFITM3 C2orf88 CD300LF AMD1 RPL7A SLC17A4 RPS23 RAB3B HIST1H1C KRT20
40 CREB3L1 CHP2 MAOA RPL4 PKM PKIB DPYSL3 AC005837.1 RPS13 TRPM6 RPS14 SYTL5 GPA33 SDCBP2
41 RPL37 LGALS2 NFIB RPS5 RPL4 FABP1 KIT ID4 RPS9 C11orf86 RPS18 LGALS9B TMIGD1 LYPD8
42 RPL32 SULT1B1 PLCB4 RPS6 DKC1 SMPDL3A TAS1R3 SOCS3 RPL37 ABCG2 TGFBI IL3RA ATP1B3 GNPTAB
43 TPSG1 TST MUC12 RPL13A CD81 CDKN2B-AS1 PIK3CG CDKN1C RPL19 ABCB1 GPX2 FAM177B UGP2 MT1X
44 ATOH1 S100A6 TXN RPS3 PPA1 MEP1A HTR3C AC007613.1 UQCRH HSD17B2 NACA SYT7 FXYD3 HEPACAM2
45 RPS8 MT1F PPP1R1B RPL14 PCNA PDZD3 VAV1 SELENBP1 PEBP1 HHLA2 RPL4 FAXDC2 LGALS3 MT1F
46 RPL13A FLNB LIMA1 RPLP0 PDIA6 PDE9A TREH AL021453.1 PRDX5 SULT1A2 RPL24 SMIM6 C11orf86 SAMHD1
47 C12orf57 ANPEP PKP2 RACK1 EIF2S2 SDCBP2 NCMAP RHOB RPL23 RHOF RPL27 CREB3L1 SLC51B PROX1
48 RPL3 MT1X ATP8B1 RPS24 GGH MT-ND1 DCLK2 POLR2A RPS27 FABP1 RPL10A TM4SF5 CLDN23 CEACAM1
49 RPL34 GPT PGM2L1 RPL19 CCT2 SLC9A3 FRY MT-ND5 RPS21 GPA33 GSTP1 IFI27 ASS1 CKB
50 RPL13 TMIGD1 TC2N RPLP1 NHP2 MDK PAK3 AC091271.1 RPL35A MXI1 RPS2 TRANK1 GUCA2B GUCY2C
51 TSPAN13 HSD11B2 PLCE1 RPL23 NUCKS1 GPA33 KCNQ4 RPS19 RPL7 PHGR1 RPL19 FAM3D TNFSF10 AOC1
52 LGALS4 AHCYL2 KCNE3 RPS27 FBL TXNIP CAMP HIST1H1E RPL13 SAMD9 RPS6 PLAC8 GPRC5A VIPR1
53 RPL28 TRPM6 ADD3 RPS14 SSB MT-ND5 CGNL1 MED29 RPL12 MDK RPSA GPRIN2 SAMD9 ECE1
54 SELENOK SFN PALLD NACA MCM3 SCNN1B C11orf53 HIST1H4E YBX1 MT-CO1 HSPD1 ISG20 UPP1 GPA33
55 RAP1GAP ACADS APP RPL5 SCD SULT1A2 ZFHX3 RPS18 RPL31 KRT20 RPL13 MUC13 MDK CDHR5
56 RPS14 AMN PDZK1IP1 RPS3A PTTG1 C1QTNF12 PLEKHB1 ELF3 RPS20 C2orf88 NPM1 MCF2L ACAA2 CLCA4
57 RPS9 PLCD3 TFCP2L1 EEF1A1 LSM5 CDHR2 CCDC28B HIST1H2BH RPS3 CFDP1 RPS3A VIPR1 SPATS2L CEACAM7
58 RPS3A TPRN PPA1 AC020656.1 PGK1 CYP3A5 SPTLC2 DDIT4 RPL28 CLDN23 RPL32 CLDN8 RHOF MALT1
59 FABP2 GIPC1 PAPSS2 NPM1 BIRC5 AAK1 BCAM AL135925.1 RPL27 PDE9A RPS13 SLC16A9 HLA-A SRI
60 GMDS SLC4A4 SQOR RPSA HMGB2 RHOU RASSF6 PCK1 ATP5MC2 PTPRR RPS3 VSIG2 SGK1 SAMD9
61 RPS6 SLC9A3 GLUL RPL9 GTF3A MXI1 ATP2A3 TCIM RPL4 PRAP1 RPL6 HLA-E HSD17B2 PDK1
62 L1TD1 CEACAM1 CES2 RPS13 IPO5 MT-CO3 EIF1B RPL13 RPL30 RFK RPLP1 SAMD9 CDA TMEM176A
63 BEST2 MISP ANXA2 RPL34 EIF3E HHLA2 FES H3F3B MLEC ENTPD8 RPL37 MFSD4A EPCAM SLC20A1
64 RPS18 SCNN1B CTSS ZFAS1 RPN2 RHOC HOTAIRM1 DNAJB1 C1QBP ATP1B3 RPS24 HEPACAM2 RFK PDE9A
65 RPS15A PRDX6 MTUS1 LYZ RNF43 IFI27 MARCKSL1 VEGFA RPL21 LINC02023 RPS16 FXYD3 CGN CFD
66 RPL9 PAPSS2 TSPO HSPD1 ANP32B NAAA SELENOM CEBPD ADH1C TNFSF10 RPS19 DDX60 SRI TMSB10
67 RPL12 UGT2B17 NFKBIZ RPL23A HSPH1 MISP MTSS1 HSPA1A NUCKS1 MYL12B RPS5 NAAA TMEM37 TMEM176B
68 RPS16 SMIM22 PYCARD RPL18A TPX2 PHGR1 TLE4 PLCE1 TMSB10 TIMP2 PHLDA2 DST DSC2 GSN
69 KRT18 CHP1 CCND1 RPL27 C1QBP CFDP1 TPM1 PMAIP1 PPP1R1B MIER3 EEF1B2 TUBB2A CLTB LINC01559
70 RPL23A CD24 CCL28 SET CBX3 FTH1 KRT18 SRSF7 RACK1 SLC6A8 KLK10 SELENOP ITM2C CEACAM6
71 RPL10A CDKN2B C15orf48 PKM RSL1D1 MIER3 IGSF3 ARGLU1 RPL22 TMPRSS2 GAPDH SCGB2A1 CTSZ DSC2
72 CKAP4 PPDPF TCEA3 RPS9 BRCA2 SMCHD1 LUC7L3 SNHG8 FABP5 DST RPL3 TPM1 CDHR2 HSD17B2
73 TCEA3 SRI BACE2 EEF1B2 ATAD5 PRSS3 TBC1D2B YME1L1 HSPD1 MXD1 RPL9 MLLT3 PRSS8 TP53INP1
74 RPS5 ITM2C MGST3 PTMS ODC1 HLA-A SLCO3A1 RND3 RPL39 HLA-A SET S100P MEP1A MDK
75 RPLP0 TP53I3 PPIC EPHB3 MCM4 FXYD3 KLK11 HNRNPU EIF3L FXYD3 PKM GDPD3 SMPDL3A PTPRR
76 HPCAL1 S100A10 HIF1A GSTP1 RAD21 CDKN2B MAP7 DUT SCNN1B SLC2A1 EIF2AK3 EFHD2 SLC17A4
77 RPL30 MVP HSPA1A COMMD6 SMC1A CTSA PTPN6 EEF1A1 SMPD1 YWHAB HLA-A ISG20 VSIR
78 RAB27A AKR1C3 PCK1 MMP7 MCM7 DST INPP5D CD99 FTH1 RPLP0 LINC01559 CHP1 S100A10
79 RPL24 CTSA LGALS2 RPL10 TGFBI CGN PTPRJ CCND2 CCDC152 RPS10 GALNT5 PPP1R14D ITM2C
80 RPL35A GPA33 GPR160 RPL36A ASCL2 TNFSF10 JMY RPL36A PRSS8 PGK1 FAM107B MXI1 TP53INP2
81 RPS4X MAOA NFIA EGR3 PRDX4 ATP1B3 FURIN IMPDH2 CDKN2B-AS1 NDUFA4 LPIN2 SLC6A8 PHGR1
82 ERN2 PRR13 UQCRH RPL22 MYC SERINC2 LIMCH1 ESD NAAA EIF2S2 FSIP2 SECTM1 FABP1
83 MLPH ID1 B3GALT5 TMSB10 FERMT1 ANKRD12 CHD6 FBL SPATS2L RACK1 MUC4 TYMP ID4
84 RPL19 AOC1 S100A10 RPS10 CDCA7 PDCD4 UTRN SNRPF CGN CCND1 MAN1A1 SERINC2 CDC42BPA
85 MYADM ACAA2 NACA PROX1 HMGB3 FCGRT ANXA1 GMNN SERINC2 HSPH1 KRT20 CTSA FXYD3
86 MUC4 CSTB LAPTM4A MACC1 RPA3 LIPH DEFB1 TRABD2A GPRC5A KRT17 KAZALD1 LMO7 MEP1A
87 RPL31 MGLL SRI HMGA1 DPEP1 TCF7L2 ERO1B APEX1 TYMP RPS8 WNK4 CDKN1A ID1
88 AC005833.1 GGT6 PI3 IFITM3 SNRPD1 PRDX6 COL9A3 EBPL MYO15B DNAJC15 CCDC68 OASL TDP2
89 ARFGEF3 RHOC PEBP1 GPX2 NOP58 SMIM22 CD14 MYB TRANK1 PDIA6 SH3BGRL3 SMPD1 KRT8
90 GNE MUC12 LPP PERP WDR34 PCK1 LIPG PTGDR DHRS9 RPN2 CD63 PDE9A ATP1B1
91 RPS23 IFI27 HLA-DRA HSPH1 CBX5 IL13RA1 AQP1 TMEM54 DPEP1 SAT1 MIER3 A1CF
92 ANXA13 CD177 ATP5MC1 SOX4 ECT2 BIK RPS25 ISG20 HMGA1 TCF7L2 ST14 FNIP2
93 FMOD TDP2 DSG2 RPL39 SMC4 MYO1B NUPR1 COL17A1 ABHD2 NEDD4L TMBIM1 MT-CO1
94 B3GNT6 MYL12B RPL10A HSP90AA1 WDR43 ARHGEF38 LBR C1orf115 RPL39 HLA-F DDX60 MISP
95 SLC4A7 VSIG2 SLC44A4 NCL CCNB1 GNAI2 LDHB UGP2 SERPINB1 SECTM1 RSAD2 NEAT1
96 ANO7 S100A14 RAB25 RNF43 HACD3 PROX1 RANBP1 SFN NORAD SDCBP2 MYH14 CA2
97 FOXA3 TMSB4X PDIA3 RPS25 PARP1 HEPACAM2 CFTR RSAD2 KRT23 LIPH XDH FLNB
98 ALDH1A1 EFHD2 GAPDH TUBA1A SMS PPDPF RPL36 LINC01559 RPL28 ANO7 PLIN3 BSG
99 IL1R2 C4orf48 PFN1 SCD FASN CAPN12 HSPE1 CDKN2B ATP6V1G1 DISP2 ABCG2 SELENOW
100 DLL1 MAPK3 RPL3 PMEPA1 CMSS1 ARGLU1 HMGCS2 DDX60 ERO1A PHGR1 TMEM45B HSPB1